BOSTON — There are legitimate concerns in the Yankees hierarchy about Michael Pineda’s right shoulder.

Pineda’s first minor league rehab start was cut short Saturday after 15 pitches because of weakness and pain in the hinge.

“Of course I am concerned,’’ said general manager Brian Cashman, who sent Jesus Montero and Hector Noesi to Seattle for the 23-year-old Pineda and 19-year-old Jose Campos with the idea that Pineda eventually would develop into a top-of-the-rotation starter.

Pineda was examined in Tampa Saturday and was sent to New York, where he will undergo a dye contrast MRI exam.

“We are treating the patient and not the MRI because the MRI [in late spring training] was clean,’’ Cashman said. “Now we are digging deeper with more invasive tests. The patient hit the wall and we want to find out the reason.’’

When Pineda was diagnosed with tendinitis in the back of the right shoulder on March 31, Cashman insisted the Yankees didn’t receive damaged goods from Seattle.

“Not good, 15 pitches and he felt the weakness in the back of the shoulder again so they took him out,’’ manager Joe Girardi said before the Yankees’ 15-9 comeback victory over the Red Sox. “He will see the doctor in Tampa on Monday and we will go from there.’’

Pineda, who was in danger of not making the rotation during the late stages of spring training, was diagnosed with tendinitis in the shoulder after a March 30 start against the Phillies in Tampa.

Yesterday was his first start since, and that it lasted 15 pitches is a red flag because during throwing sessions on flat ground and off bullpen mounds Pineda hadn’t experienced discomfort, pain or weakness.

“That’s one thing you can’t control, when the intensity turns up how a guy is going to feel,’’ Girardi said.

Before yesterday’s setback, Pineda wasn’t expected back until the end of May at the earliest. Now, depending on what is uncovered tomorrow who knows when Pineda returns.

Pineda’s entry into the Yankees’ universe couldn’t have gone worse. He reported to camp admitting to weighing 280 pounds which he said was 10 more than he ended last year, his rookie season. However, the Mariners’ 2011 media guide and the Yankees’ guide this season list him at 260.

Immediately, questions about a lack of velocity surfaced and followed him throughout the exhibition season. Then, after getting rocked by the Phillies, he was hurt. Some believe he suffered the problem by over-throwing trying to increase the fastball velocity from the low 90s to the mid-90s where it was in the first half of last season.

“I think it’s somewhat significant because you were expecting him to build up,’’ Girardi said of the setback. “Now we have to give him more time than we did before. I can’t tell you when we will get him back now.’’

Though Pineda wasn’t on the immediate big league radar, the belief was that by late May or early June he could be in the rotation.

Andy Pettitte is moving through a minor league rehab program and is in line for an early to mid-May return to the big leagues after sitting out last season.

The favorite to be deleted is Freddy Garcia, after he was bounced by the Red Sox yesterday in the second inning and is sporting a 9.75 ERA in three starts.